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Song Z, Zhou S, Zhang H, Keller NP, Oakley BR, Liu X, Yin WB. Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex. Nat Commun 2023; 14:7351. [PMID: 37963872 PMCID: PMC10645843 DOI: 10.1038/s41467-023-43205-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 11/03/2023] [Indexed: 11/16/2023] Open
Abstract
Production of secondary metabolites is controlled by a complicated regulatory network in eukaryotic cells. Several layers of regulators are involved in this process, ranging from pathway-specific regulation, to epigenetic control, to global regulation. Here, we discover that interaction of an RNA-binding protein CsdA with a regulator RsdA coordinates fungal secondary metabolism. Employing a genetic deletion approach and transcriptome analysis as well as metabolomics analysis, we reveal that CsdA and RsdA synergistically regulate fungal secondary metabolism comprehensively. Mechanistically, comprehensive genetic and biochemical studies prove that RsdA and CsdA co-localize in the nucleus and physically interact to achieve their functions. In particular, we demonstrate that CsdA mediates rsdA expression by binding specific motif "GUCGGUAU" of its pre-mRNA at a post-transcriptional level. We thus uncover a mechanism in which RNA-binding protein physically interacts with, and controls the expression level of, the RsdA to coordinate fungal secondary metabolism.
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Affiliation(s)
- Zili Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, PR China
| | - Shuang Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Hongjiao Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, PR China
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, PR China.
- Savaid Medical School, University of Chinese Academy of Sciences, 100049, Beijing, PR China.
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2
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Seven Years at High Salinity-Experimental Evolution of the Extremely Halotolerant Black Yeast Hortaea werneckii. J Fungi (Basel) 2021; 7:jof7090723. [PMID: 34575761 PMCID: PMC8468603 DOI: 10.3390/jof7090723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 01/26/2023] Open
Abstract
The experimental evolution of microorganisms exposed to extreme conditions can provide insight into cellular adaptation to stress. Typically, stress-sensitive species are exposed to stress over many generations and then examined for improvements in their stress tolerance. In contrast, when starting with an already stress-tolerant progenitor there may be less room for further improvement, it may still be able to tweak its cellular machinery to increase extremotolerance, perhaps at the cost of poorer performance under non-extreme conditions. To investigate these possibilities, a strain of extremely halotolerant black yeast Hortaea werneckii was grown for over seven years through at least 800 generations in a medium containing 4.3 M NaCl. Although this salinity is well above the optimum (0.8–1.7 M) for the species, the growth rate of the evolved H. werneckii did not change in the absence of salt or at high concentrations of NaCl, KCl, sorbitol, or glycerol. Other phenotypic traits did change during the course of the experimental evolution, including fewer multicellular chains in the evolved strains, significantly narrower cells, increased resistance to caspofungin, and altered melanisation. Whole-genome sequencing revealed the occurrence of multiple aneuploidies during the experimental evolution of the otherwise diploid H. werneckii. A significant overrepresentation of several gene groups was observed in aneuploid regions. Taken together, these changes suggest that long-term growth at extreme salinity led to alterations in cell wall and morphology, signalling pathways, and the pentose phosphate cycle. Although there is currently limited evidence for the adaptive value of these changes, they offer promising starting points for future studies of fungal halotolerance.
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John E, Singh KB, Oliver RP, Tan K. Transcription factor control of virulence in phytopathogenic fungi. MOLECULAR PLANT PATHOLOGY 2021; 22:858-881. [PMID: 33973705 PMCID: PMC8232033 DOI: 10.1111/mpp.13056] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Karam B. Singh
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern AustraliaAustralia
| | - Richard P. Oliver
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kar‐Chun Tan
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
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Herold I, Zolti A, Garduño-Rosales M, Wang Z, López-Giráldez F, Mouriño-Pérez RR, Townsend JP, Ulitsky I, Yarden O. The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassa. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:672696. [PMID: 37744127 PMCID: PMC10512220 DOI: 10.3389/ffunb.2021.672696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 09/26/2023]
Abstract
The Neurospora crassa GUL-1 is part of the COT-1 pathway, which plays key roles in regulating polar hyphal growth and cell wall remodeling. We show that GUL-1 is a bona fide RNA-binding protein (RBP) that can associate with 828 "core" mRNA species. When cell wall integrity (CWI) is challenged, expression of over 25% of genomic RNA species are modulated (2,628 mRNAs, including the GUL-1 mRNA). GUL-1 binds mRNAs of genes related to translation, cell wall remodeling, circadian clock, endoplasmic reticulum (ER), as well as CWI and MAPK pathway components. GUL-1 interacts with over 100 different proteins, including stress-granule and P-body proteins, ER components and components of the MAPK, COT-1, and STRIPAK complexes. Several additional RBPs were also shown to physically interact with GUL-1. Under stress conditions, GUL-1 can localize to the ER and affect the CWI pathway-evident via altered phosphorylation levels of MAK-1, interaction with mak-1 transcript, and involvement in the expression level of the transcription factor adv-1. We conclude that GUL-1 functions in multiple cellular processes, including the regulation of cell wall remodeling, via a mechanism associated with the MAK-1 pathway and stress-response.
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Affiliation(s)
- Inbal Herold
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avihai Zolti
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Marisela Garduño-Rosales
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Ensenada, Mexico
| | - Zheng Wang
- Department of Biostatistics, Yale University, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Francesc López-Giráldez
- Yale Center for Genome Analysis, Department of Genetics, Yale University, New Haven, CT, United States
| | - Rosa R. Mouriño-Pérez
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Ensenada, Mexico
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale University, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Jacquat AG, Theumer MG, Cañizares MC, Debat HJ, Iglesias J, García Pedrajas MD, Dambolena JS. A Survey of Mycoviral Infection in Fusarium spp. Isolated from Maize and Sorghum in Argentina Identifies the First Mycovirus from Fusarium verticillioides. Viruses 2020; 12:v12101161. [PMID: 33066620 PMCID: PMC7602464 DOI: 10.3390/v12101161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
Mycoviruses appear to be widespread in Fusarium species worldwide. The aim of this work was to identify mycoviral infections in Fusarium spp., isolated from maize and sorghum grown in Argentina, and to estimate their potential effects on the pathogenicity and toxigenesis of the host fungus towards maize. Mycoviruses were identified in 2 out of 105 isolates analyzed; Fusarium verticillioides strain Sec505 and Fusarium andiyazi strain 162. They were characterized as members of the genus Mitovirus by high-throughput sequencing and sequence analysis. The F. verticillioides mitovirus was a novel mycovirus whereas the F. andiyazi mitovirus was found to be a new strain of a previously identified mitovirus. We have named these mitoviruses, Fusarium verticillioides mitovirus 1 (FvMV1) and Fusarium andiyazi mitovirus 1 strain 162 (FaMV1-162). To our knowledge, FvMV1 is the first mycovirus reported as naturally infecting F. verticillioides, the major causal agent of ear rot and fumonisin producer in corn. Both mitoviruses exhibited 100% vertical transmission rate to microconidia. The Fa162 strain infected with FaMV1-162 did not show phenotypic alterations. In contract, F. verticillioides Sec505 infected with FvMV1 showed increased virulence as well as microconidia and fumonisin-B1 production, compared with two uninfected strains. These results suggest that FvMV1 could have a role in modulating F. verticillioides pathogenicity and toxin production worth further exploring.
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Affiliation(s)
- Andrés Gustavo Jacquat
- Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Vélez Sarsfield 1611, Córdoba X5016GCA, Argentina
| | - Martín Gustavo Theumer
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas (FCQ), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Haya de la Torre y Medina Allende—Ciudad Universitaria, Córdoba X5000HUA, Argentina
| | - María Carmen Cañizares
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM—UMA—CSIC), Estación Experimental “La Mayora”, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
| | - Humberto Julio Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5.5, Córdoba X5020ICA, Argentina;
| | - Juliana Iglesias
- Estación Experimental Pergamino, (EEA) INTA Pergamino, Universidad Nacional Noroeste (UNNOBA), Pergamino (Buenos Aires) B2700, Argentina;
| | - María Dolores García Pedrajas
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM—UMA—CSIC), Estación Experimental “La Mayora”, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
- Correspondence: (M.D.G.P.); (J.S.D.)
| | - José Sebastián Dambolena
- Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Vélez Sarsfield 1611, Córdoba X5016GCA, Argentina
- Correspondence: (M.D.G.P.); (J.S.D.)
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Wan PJ, Zhou RN, Nanda S, He JC, Yuan SY, Wang WX, Lai FX, Fu Q. Phenotypic and transcriptomic responses of two Nilaparvata lugens populations to the Mudgo rice containing Bph1. Sci Rep 2019; 9:14049. [PMID: 31575938 PMCID: PMC6773769 DOI: 10.1038/s41598-019-50632-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/17/2019] [Indexed: 11/08/2022] Open
Abstract
The Bph1 gene was the first reported brown planthopper (BPH, Nilaparvata lugens) resistance gene in Mudgo rice and was widely used as a commercial cultivar for controlling BPH infestations. However, rapid adaptations of BPH on the Mudgo rice resulted in its resistance breakdown and the emergence of virulent BPH populations. Thus, specific BPH populations and rice varieties can serve as good model systems for studying the roles of different bio-compounds and proteins in the insect-plant interactions. Although our understandings have been improved on the complexity of BPH and rice interactions, the underlying molecular mechanisms remain largely unknown. Here we analyzed the feeding performances and the transcriptomic responses of two BPH populations (Mugdo-BPH and TN1-BPH) during compatible (Mudog-BPH feeding on Mudgo rice) and incompatible (TN1-BPH feeding on Mudgo rice) interactions. The electrical penetration graph (EPG) results indicated that the BPH feeding and performances during the incompatible interaction are significantly affected in terms of decreased honeydew, loss of weight, decreased phloem sap ingestion (N4 waveform), but increased non-penetration (NP waveform) phase. Abundance of glucose and trehalose was reduced in BPH during the incompatible interaction. Transcriptomic surveys of insects in both interactions revealed that genes involved in cuticle formation, detoxification, metabolite transport, digestion, RNA processing, lipid or fatty acid metabolism, and proteolysis were significantly down-regulated during the incompatible interaction, whereas genes involved in insulin signaling were significantly upregulated. Knockdown of four genes, including the sugar transporter NlST45, the serine and arginine-rich protein NlSRp54, the cytochrome P450 gene NlCYP6AY1, and the cuticle protein NlCPR70 through RNA-interference revealed thess genes are important for BPH survival. Overall, the results of this study will be helpful for the future researches on BPH virulence shifts.
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Affiliation(s)
- Pin-Jun Wan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Ruo-Nan Zhou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Satyabrata Nanda
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jia-Chun He
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - San-Yue Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Wei-Xia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Feng-Xiang Lai
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qiang Fu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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Rodríguez-Romero J, Marconi M, Ortega-Campayo V, Demuez M, Wilkinson MD, Sesma A. Virulence- and signaling-associated genes display a preference for long 3'UTRs during rice infection and metabolic stress in the rice blast fungus. THE NEW PHYTOLOGIST 2019; 221:399-414. [PMID: 30169888 DOI: 10.1111/nph.15405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
Generation of mRNA isoforms by alternative polyadenylation (APA) and their involvement in regulation of fungal cellular processes, including virulence, remains elusive. Here, we investigated genome-wide polyadenylation site (PAS) selection in the rice blast fungus to understand how APA regulates pathogenicity. More than half of Magnaporthe oryzae transcripts undergo APA and show novel motifs in their PAS region. Transcripts with shorter 3'UTRs are more stable and abundant in polysomal fractions, suggesting they are being translated more efficiently. Importantly, rice colonization increases the use of distal PASs of pathogenicity genes, especially those participating in signalling pathways like 14-3-3B, whose long 3'UTR is required for infection. Cleavage factor I (CFI) Rbp35 regulates expression and distal PAS selection of virulence and signalling-associated genes, tRNAs and transposable elements, pointing its potential to drive genomic rearrangements and pathogen evolution. We propose a noncanonical PAS selection mechanism for Rbp35 that recognizes UGUAH, unlike humans, without CFI25. Our results showed that APA controls turnover and translation of transcripts involved in fungal growth and environmental adaptation. Furthermore, these data provide useful information for enhancing genome annotations and for cross-species comparisons of PASs and PAS usage within the fungal kingdom and the tree of life.
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Affiliation(s)
- Julio Rodríguez-Romero
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Marco Marconi
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Víctor Ortega-Campayo
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Marie Demuez
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Mark D Wilkinson
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
| | - Ane Sesma
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Universidad Politécnica de Madrid (UPM) & Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología y Biología Vegetal, UPM, Campus Ciudad Universitaria, 28040, Madrid, Spain
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